I will probably, eventually, have a traditional shoe made with the through bolts. For now I am fabricating the bottom plate and have it screwed up into the skeg. I am going to glass it as well which will make the removal difficult when I want to drop my rudder next year.
I would advise not 'glassing it but attaching it mechanically. When I repaired one of these after Superstorm Sandy I bolted the original skeg back into the hull (with sufficient backing plates) but these became inaccessible bolts - had to cut 3" round hole in skin of skeg to hold them with wrench. When the hole was 'glassed over it made no sense to retain the accessibility and so the whole skeg was 'glassed to the hull.
I would recommend a structure by which the fiberglass skeg is permanently 'glassed to the hull and the metal 'shoe' is stuck to the bottom with 5200. This shoe should have an SS rod, with threads and a nut on bottom, going straight up through the skeg to the inside of the boat where it is retained by another plate and another nut on top. This could as well be a blade too, with more than one nut; but then it would not be removable for inspection and repair (with my way you could drop the rod out the bottom of the skeg if you lift the boat high enough, such as by TravelLift). Make the rod about 5/8" or 3/4". Use only US-made type-304 stainless steel. Paint all the underwater SS surfaces in epoxy paint and be sure to fit a cotter pin (a heavy one) to the bottom of the shaft. This will entail some drag; which can be compensated-for by a little thin 'glass cover tacked over the end with sheet-metal screws.
I would not worry about keeping water out of the skeg - though SS immersed in seawater is never good - but would provide a drain hole in the bottom of the fiberglass skeg so it can be drained. If you were really cool you'd provide a drain plug at the top end too and flush it with fresh water from the garden hose every haul-out. Still, the SS will need constant vigilance and should be removed and inspected maybe every 6-8 years - hence my insisting on the nuts for the rod, rather than threading it into the SS plates - or, worse, welding it all as one.
Now; if you could have the whole thing made in marine bronze....